The MEME suite: motif based sequence analysis tools

The MEME Suite allows the biologist to discover novel motifs in
collections of unaligned nucleotide or protein sequences, and to perform
a wide variety of other motif-based analyses. The Suite supports motif-
based analysis of DNA, RNA and protein sequences. It provides motif
discovery algorithms using both probabilistic (MEME) and discrete models
(MEME), which have complementary strengths. It also allows discovery of
motifs with arbitrary insertions and deletions (GLAM2). In addition to
motif discovery, the MEME Suite provides tools for scanning sequences
for matches to motifs (FIMO, MAST and GLAM2Scan), scanning for clusters
of motifs (MCAST), comparing motifs to known motifs (Tomtom), finding
preferred spacings between motifs (SpaMo), predicting the biological
roles of motifs (GOMo), measuring the positional enrichment of sequences
for known motifs (CentriMo), and analyzing ChIP-seq and other large
datasets (MEME-ChIP).

Check README.TESTS for runing the recommended tests on the compiled
executables. Here, the tests *FAIL* on a 32bit system!

Check README.DATABASES for more info or if you want to install
meme-suite without the databases present at build time.

To cite the full MEME suite:
Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles
E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, 
"MEME SUITE: tools for motif discovery and searching", Nucleic Acids
Research, 37:W202-W208, 2009.

To cite individual tools, please check the citation page:
http://meme-suite.org/doc/cite.html